marker-assisted breeding for rice improvement bert collard & david mackill plant breeding,...
TRANSCRIPT
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MARKER-ASSISTED BREEDING FOR RICE IMPROVEMENT
Bert Collard & David MackillPlant Breeding, Genetics and Biotechnology (PBGB) Division, IRRI
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LECTURE OUTLINE
1. MARKER ASSISTED SELECTION: THEORY AND PRACTICE
2. MAS BREEDING SCHEMES
3. IRRI CASE STUDY
4. CURRENT STATUS OF MAS
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SECTION 1
MARKER ASSISTED SELECTION (MAS):
THEORY AND PRACTICE
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Definition:
Marker assisted selection (MAS) refers to the use of DNA markers that are tightly-linked to target loci as a substitute for or to assist phenotypic screening
Assumption: DNA markers can reliably predict phenotype
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F2
P2
F1
P1 x
large populations consisting of thousands of plants
PHENOTYPIC SELECTION
Field trialsGlasshouse trials
DonorRecipient
CONVENTIONAL PLANT BREEDING
Salinity screening in phytotron Bacterial blight screening Phosphorus deficiency plot
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F2
P2
F1
P1 x
large populations consisting of thousands of plants
ResistantSusceptible
MARKER-ASSISTED SELECTION (MAS)
MARKER-ASSISTED BREEDING
Method whereby phenotypic selection is based on DNA markers
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Advantages of MAS• Simpler method compared to
phenotypic screening– Especially for traits with laborious screening– May save time and resources
• Selection at seedling stage– Important for traits such as grain quality– Can select before transplanting in rice
• Increased reliability– No environmental effects– Can discriminate between homozygotes and
heterozygotes and select single plants
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Potential benefits from MAS
• more accurate and efficient selection of specific genotypes– May lead to
accelerated variety development
• more efficient use of resources– Especially field trials
Crossing house
Backcross nursery
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(1) LEAF TISSUE SAMPLING
(2) DNA EXTRACTION
(3) PCR
(4) GEL ELECTROPHORESIS
(5) MARKER ANALYSIS
Overview of ‘marker
genotyping’
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Considerations for using DNA markers in plant breeding
• Technical methodology– simple or complicated?
• Reliability• Degree of polymorphism• DNA quality and quantity required• Cost**• Available resources
– Equipment, technical expertise
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Markers must be tightly-linked to target loci!
• Ideally markers should be <5 cM from a gene or QTL
• Using a pair of flanking markers can greatly improve reliability but increases time and cost
Marker A
QTL5 cM
RELIABILITY FOR SELECTION
Using marker A only:
1 – rA = ~95%
Marker A
QTL
Marker B
5 cM 5 cM
Using markers A and B:
1 - 2 rArB = ~99.5%
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Markers must be polymorphic
1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8RM84 RM296
P1 P2
P1 P2
Not polymorphic Polymorphic!
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DNA extractions
DNA EXTRACTIONS
LEAF SAMPLING
Porcelain grinding plates
High throughput DNA extractions “Geno-Grinder”
Mortar and pestles
Wheat seedling tissue sampling in Southern Queensland, Australia.
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PCR-based DNA markers• Generated by using Polymerase Chain Reaction• Preferred markers due to technical simplicity and cost
GEL ELECTROPHORESISAgarose or Acrylamide gels
PCR
PCR Buffer +
MgCl2 +
dNTPS +
Taq +
Primers +
DNA template
THERMAL CYCLING
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Agarose gel electrophoresis
http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/gels/agardna.html
UV light
UV transilluminator
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UV light
UV transilluminator
Acrylamide gel electrophoresis 1
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Acrylamide gel electrophoresis 2
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SECTION 2
MAS BREEDING SCHEMES
1. Marker-assisted backcrossing
2. Pyramiding
3. Early generation selection
4. ‘Combined’ approaches
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2.1 Marker-assisted backcrossing (MAB)
• MAB has several advantages over conventional backcrossing:– Effective selection of target loci– Minimize linkage drag– Accelerated recovery of recurrent parent
1
2 3 4
Target locus
1
2 3 4
RECOMBINANT SELECTION
1
2 3 4
BACKGROUND SELECTION
TARGET LOCUS SELECTION
FOREGROUND SELECTION
BACKGROUND SELECTION
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2.2 Pyramiding• Widely used for combining multiple disease
resistance genes for specific races of a pathogen
• Pyramiding is extremely difficult to achieve using conventional methods– Consider: phenotyping a single plant for multiple
forms of seedling resistance – almost impossible
• Important to develop ‘durable’ disease resistance against different races
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F2
F1
Gene A + B
P1
Gene A
x P1
Gene B
MAS
Select F2 plants that have Gene A and Gene B
Genotypes
P1: AAbb P2: aaBB
F1: AaBb
F2AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB AaBB AaBb aaBB aaBb
ab AaBb Aabb aaBb aabb
• Process of combining several genes, usually from 2 different parents, together into a single genotype
x
Breeding plan
Hittalmani et al. (2000). Fine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in riceTheor. Appl. Genet. 100: 1121-1128
Liu et al. (2000). Molecular marker-facilitated pyramiding of different genes for powdery mildew resistance in wheat. Plant Breeding 119: 21-24.
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2.3 Early generation MAS
• MAS conducted at F2 or F3 stage• Plants with desirable genes/QTLs are
selected and alleles can be ‘fixed’ in the homozygous state– plants with undesirable gene combinations can be
discarded
• Advantage for later stages of breeding program because resources can be used to focus on fewer lines
References:
Ribaut & Betran (1999). Single large-scale marker assisted selection (SLS-MAS). Mol Breeding 5: 21-24.
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F2
P2
F1
P1 x
large populations (e.g. 2000 plants)
ResistantSusceptible
MAS for 1 QTL – 75% elimination of (3/4) unwanted genotypes
MAS for 2 QTLs – 94% elimination of (15/16) unwanted genotypes
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P1 x P2
F1
PEDIGREE METHOD
F2
F3
F4
F5
F6
F7
F8 – F12
Phenotypic screening
Plants space-planted in rows for individual plant selection
Families grown in progeny rows for selection.
Preliminary yield trials. Select single plants.
Further yield trials
Multi-location testing, licensing, seed increase and cultivar release
P1 x P2
F1
F2
F3
MAS
SINGLE-LARGE SCALE MARKER-ASSISTED SELECTION (SLS-MAS)
F4Families grown in progeny rows for selection.
Pedigree selection based on local needs
F6
F7
F5
F8 – F12Multi-location testing, licensing, seed increase and cultivar release
Only desirable F3 lines planted in field
Benefits: breeding program can be efficiently scaled down to focus on fewer lines
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2.4 Combined approaches
• In some cases, a combination of phenotypic screening and MAS approach may be useful
1. To maximize genetic gain (when some QTLs have been unidentified from QTL mapping)
2. Level of recombination between marker and QTL (in other words marker is not 100% accurate)
3. To reduce population sizes for traits where marker genotyping is cheaper or easier than phenotypic screening
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‘Marker-directed’ phenotyping
BC1F1 phenotypes: R and S
P1 (S) x P2 (R)
F1 (R) x P1 (S)
RecurrentParent
DonorParent
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 …
SAVE TIME & REDUCE COSTS
*Especially for quality traits*
MARKER-ASSISTED SELECTION (MAS)
PHENOTYPIC SELECTION
(Also called ‘tandem selection’)
• Use when markers are not 100% accurate or when phenotypic screening is more expensive compared to marker genotyping
References:
Han et al (1997). Molecular marker-assisted selection for malting quality traits in barley. Mol Breeding 6: 427-437.
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Any questions
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SECTION 3
IRRI MAS CASE STUDY
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3. Marker-assisted backcrossing for submergence tolerance
David Mackill, Reycel Mighirang-Rodrigez, Varoy Pamplona, CN Neeraja, Sigrid Heuer, Iftekhar Khandakar, Darlene
Sanchez, Endang Septiningsih & Abdel Ismail
Photo by Abdel Ismail
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Abiotic stresses are major constraints to rice production in SE Asia
• Rice is often grown in unfavourable environments in Asia
• Major abiotic constraints include:– Drought– Submergence– Salinity– Phosphorus deficiency
• High priority at IRRI• Sources of tolerance for all traits in germplasm and
major QTLs and tightly-linked DNA markers have been identified for several traits
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‘Mega varieties’
• Many popular and widely-grown rice varieties - “Mega varieties”– Extremely popular with farmers
• Traditional varieties with levels of abiotic stress tolerance exist however, farmers are reluctant to use other varieties– poor agronomic and quality
characteristics
BR11 Bangladesh
CR1009 India
IR64 All Asia
KDML105 Thailand
Mahsuri India
MTU1010 India
RD6 Thailand
Samba Mahsuri
India
Swarna India, Bangladesh
1-10 Million hectares
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Backcrossing strategy• Adopt backcrossing strategy for incorporating
genes/QTLs into ‘mega varieties’• Utilize DNA markers for backcrossing for greater
efficiency – marker assisted backcrossing (MAB)
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Conventional backcrossingx P2P1
DonorElite cultivarDesirable trait
e.g. disease resistance
• High yielding
• Susceptible for 1 trait
• Called recurrent parent (RP)
P1 x F1
P1 x BC1
P1 x BC2
P1 x BC3
P1 x BC4
P1 x BC5
P1 x BC6
BC6F2
Visually select BC1 progeny that resemble RP
Discard ~50% BC1
Repeat process until BC6
Recurrent parent genome recovered
Additional backcrosses may be required due to linkage drag
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MAB: 1ST LEVEL OF SELECTION – FOREGROUND SELECTION
• Selection for target gene or QTL
• Useful for traits that are difficult to evaluate
• Also useful for recessive genes
1 2 3 4
Target locus
TARGET LOCUS SELECTION
FOREGROUND SELECTION
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Donor/F1 BC1
c
BC3 BC10
TARGET LOCUS
RECURRENT PARENT CHROMOSOME
DONOR CHROMOSOME
TARGET LOCUS
LIN
KE
D D
ON
OR
G
EN
ES
Concept of ‘linkage drag’ • Large amounts of donor chromosome remain even after many backcrosses• Undesirable due to other donor genes that negatively affect agronomic performance
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Conventional backcrossing
Marker-assisted backcrossing
F1 BC1
c
BC2
c
BC3 BC10 BC20
F1
c
BC1 BC2
• Markers can be used to greatly minimize the amount of donor chromosome….but how?
TARGET GENE
TARGET GENE
Ribaut, J.-M. & Hoisington, D. 1998 Marker-assisted selection: new tools and strategies. Trends Plant Sci. 3, 236-239.
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MAB: 2ND LEVEL OF SELECTION - RECOMBINANT SELECTION
• Use flanking markers to select recombinants between the target locus and flanking marker
• Linkage drag is minimized• Require large population
sizes– depends on distance of
flanking markers from target locus)
• Important when donor is a traditional variety
RECOMBINANT SELECTION
1 2 3 4
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OR
Step 1 – select target locus
Step 2 – select recombinant on either side of target locus
BC1
OR
BC2
Step 4 – select for other recombinant on either side of target locus
Step 3 – select target locus again
* *
* Marker locus is fixed for recurrent parent (i.e. homozygous) so does not need to be selected for in BC2
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MAB: 3RD LEVEL OF SELECTION - BACKGROUND SELECTION
• Use unlinked markers to select against donor
• Accelerates the recovery of the recurrent parent genome
• Savings of 2, 3 or even 4 backcross generations may be possible
1 2 3 4
BACKGROUND SELECTION
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Background selection
Percentage of RP genome after backcrossing
Theoretical proportion of the recurrent parent genome is given by the formula:
Where n = number of backcrosses, assuming large population sizes
2n+1 - 1
2n+1
Important concept: although the average percentage of the recurrent parent is 75% for BC1, some individual plants possess more or less RP than others
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P1 x F1
P1 x P2
CONVENTIONAL BACKCROSSING
BC1 VISUAL SELECTION OF BC1 PLANTS THAT MOST CLOSELY RESEMBLE RECURRENT
PARENT
BC2
MARKER-ASSISTED BACKCROSSING
P1 x F1
P1 x P2
BC1 USE ‘BACKGROUND’ MARKERS TO SELECT PLANTS THAT HAVE MOST RP MARKERS AND SMALLEST %
OF DONOR GENOME
BC2
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Breeding for submergence tolerance
• Large areas of rainfed lowland rice have short-term submergence (eastern India to SE Asia); > 10 m ha
• Even favorable areas have short-term flooding problems in some years
• Distinguished from other types of flooding tolerance– elongation ability– anaerobic germination tolerance
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Screening for submergence tolerance
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A major QTL on chrom. 9 for submergence tolerance – Sub1 QTL
1 2 3 4 5 6 7 8 90
5
10
15
20
Submergence tolerance score
IR40931-26 PI543851
Segregation in an F3 population
0 10 20 30 40
LOD score
50cM
100cM
150cM
OPN4
OPAB16
C1232
RZ698
OPS14RG553
R1016RZ206
RZ422
C985
RG570
RG451
RZ404
Sub-1(t)
1200
850
900
OPH7950
OPQ1600
Xu and Mackill (1996) Mol Breed 2: 219
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Make the backcrosses
SwarnaPopular variety
X
IR49830Sub1 donor
F1 X Swarna
BC1F1
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Pre-germinate the F1 seeds and seedthem in the seedboxes
Seeding BC1F1s
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Collect the leaf samples - 10 days after transplanting for marker analysis
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Genotyping to select the BC1F1 plants with a desired character for crosses
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Seed increase of tolerant BC2F2 plant
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Selection for Swarna+Sub1
Swarna/IR49830 F1
Swarna
BC1F1697 plants
Plant #242
Swarna
376 had Sub121 recombinantSelect plant with fewest donor alleles
158 had Sub15 recombinant
SwarnaPlant #227
BC3F118 plants
1 plant Sub1 with2 donor segments
BC2F1320 plants
Plants #246 and #81
Plant 237BC2F2
BC2F2937 plants
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Time frame for “enhancing” mega-varieties
May need to continue until BC3F2
• Name of process: “variety enhancement” (by D. Mackill)
• Process also called “line conversion” (Ribaut et al. 2002)
Mackill et al 2006. QTLs in rice breeding: examples for abiotic stresses. Paper presented at the Fifth International Rice Genetics Symposium.
Ribaut et al. 2002. Ribaut, J.-M., C. Jiang & D. Hoisington, 2002. Simulation experiments on efficiencies of gene introgression by backcrossing. Crop Sci 42: 557–565.
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Swarna with Sub1
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Graphical genotype of Swarna-Sub1
BC3F2 lineApproximately 2.9 MB of donor DNA
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Swarna 246-237
Percent chalky grains
Chalk(0-10%)=84.9
Chalk(10-25%)=9.1
Chalk(25-50%)=3.5
Chalk(>75%)=2.1
Chalk(0-10%)=93.3
Chalk(10-25%)=2.3
Chalk(25-50%)=3.7
Chalk(>75%)=0.8
Average length=0.2mm Average length=0.2mm
Average width=2.3mm Average width=2.2mm
Amylose content (%)=25
Gel temperature=HI/I
Gel consistency=98
Amylose content (%)=25
Gel temperature=I
Gel consistency=92
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IBf locus on tip of chrom 9:inhibitor of brown furrows
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Some considerations for MAB• IRRI’s goal: several “enhanced Mega varieties”• Main considerations:
– Cost– Labour– Resources– Efficiency– Timeframe
• Strategies for optimization of MAB process important– Number of BC generations– Reducing marker data points (MDP)– Strategies for 2 or more genes/QTLs
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SECTION 4
CURRENT STATUS OF MAS: OBSTACLES AND
CHALLENGES
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Current status of molecular breeding
• A literature review indicates thousands of QTL mapping studies but not many actual reports of the application of MAS in breeding
• Why is this the case?
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Some possible reasons to explain the low impact of MAS in crop
improvement• Resources (equipment) not available• Markers may not be cost-effective• Accuracy of QTL mapping studies• QTL effects may depend on genetic background
or be influenced by environmental conditions• Lack of marker polymorphism in breeding
material• Poor integration of molecular genetics and
conventional breeding
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Cost - a major obstacle• Cost-efficiency has rarely been
calculated but MAS is more expensive for most traits– Exceptions include quality traits
• Determined by:– Trait and method for phenotypic
screening– Cost of glasshouse/field trials– Labour costs– Type of markers used
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How much does MAS cost?
Institute Country Crop Cost estimate per sample*
(US$)
Reference
Uni. Guelph Canada Bean 2.74 Yu et al. (2000)
CIMMYT Mexico Maize 1.24–2.26 Dreher et al. (2003)
Uni. Adelaide Australia Wheat 1.46 Kuchel et al. (2005)
Uni. Kentucky, Uni. Minnesota, Uni.
Oregon, Michigan State Uni., USDA-
ARS
United States
Wheat and barley
0.50–5.00 Van Sanford et al. (2001)
*cost includes labour
Yu et al. 2000 Plant Breed. 119, 411-415; Dreher et al. 2003 Mol. Breed. 11, 221-234; Kuchel et al. 2005 Mol. Breed. 16, 67-78; and Van Sanford et al. 2001 Crop Sci. 41, 638-644.
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How much does MAS cost at IRRI?Consumables:• Genome mapping lab (GML) ESTIMATE
– USD $0.26 per sample (minimum costs)– Breakdown of costs: DNA extraction: 19.1%; PCR:
61.6%; Gel electrophoresis: 19.2%– Estimate excludes delivery fees, gloves, paper tissue,
electricity, water, waste disposal and no re-runs• GAMMA Lab estimate = USD $0.86 per sample
Labour:– USD $0.06 per sample (Research Technician)– USD $0.65 per sample (Postdoctoral Research Fellow)
TOTAL: USD $0.32/sample (RT); USD $0.91/sample (PDF)
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F2
P2
F1
P1 x
2000 plants
USD $640 to screen 2000 plants with a single marker for one population
Cost of MAS in context: Example 1: Early generation MAS
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Cost of MAS in context: Example 2 - Swarna+Sub1
Swarna/IR49830 F1
Swarna
BC1F1697 plants
Plant #242
Swarna376 had Sub121 recombinant
Background selection – 57
markers
158 had Sub15 recombinant23 background markers
BC2F1320 plantsEstimated minimum
costs for CONSUMABLES ONLY.
Foreground, recombinant and background BC1- BC3F2 selection = USD $2201
Plant #246
Swarna
BC3F118 plants
11 plant with Sub110 background markers
Swarna+Sub1
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Cost of MAS in contextExample 1: Pedigree selection
(2000 F2 plants) = USD $640– Philippines (Peso) = 35,200– India (Rupee) = 28,800– Bangladesh (Taka) = 44,800– Iran (Tuman) = 576,000
Example 2: Swarna+Sub1 development = USD $2201 (*consumables only)– Philippines (Peso) = 121,055– India (Rupee) = 99,045– Bangladesh (Taka) = 154,070– Iran (Tuman) = 1,980,900
• Costs quickly add up!
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A closer look at the examples of MAS indicates one common
factor:
• Most DNA markers have been developed for….
• In other words, not QTLs!! QTLs are much harder to characterize!– An exception is Sub1
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Reliability of QTL mapping is critical to the success of MAS
• Reliable phenotypic data critical!– Multiple replications and environments
• Confirmation of QTL results in independent populations
• “Marker validation” must be performed– Testing reliability for markers to predict phenotype– Testing level of polymorphism of markers
• Effects of genetic background need to be determined
Recommended references:
Young (1999). A cautiously optimistic vision for marker-assisted breeding. Mol Breeding 5: 505-510.
**Holland, J. B. 2004 Implementation of molecular markers for quantitative traits in breeding programs - challenges and opportunities. Proceedings of the 4th International Crop Sci. Congress., Brisbane, Australia.
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Breeders’ QTL mapping ‘checklist’
1. What is the population size used for QTL mapping?
2. How reliable is the phenotypic data?
– Heritability estimates will be useful
– Level of replication
3. Any confirmation of QTL results?
4. Have effects of genetic background been tested?
5. Are markers polymorphic in breeders’ material?
6. How useful are the markers for predicting phenotype? Has this been evaluated?
• LOD & R2 values will give us a good initial idea but probably more important factors include:
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Integration of molecular biology and plant breeding is often lacking
• Large ‘gaps’ remain between marker development and plant breeding– QTL mapping/marker development have been
separated from breeding– Effective transfer of data or information between
research institute and breeding station may not occur
• Essential concepts in may not be understood by molecular biologists and breeders (and other disciplines)
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Advanced backcross QTL analysis• Combine QTL mapping
and breeding together • ‘Advanced backcross
QTL analysis’ by Tanksley & Nelson (1996).– Use backcross mapping
populations– QTL analysis in BC2 or
BC3 stage– Further develop promising
lines based on QTL analysis for breeding
References:
Tanksley & Nelson (1996). Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor. Appl. Genet. 92: 191-203.
Toojinda et al. (1998) Introgression of quantitative trait loci (QTLs) determining stripe rust resistance in barley: an example of marker-assisted line development. Theor. Appl. Genet. 96: 123-131.
x P2P1
P1 x F1
P1 x BC1
BC2 QTL MAPPING
Breeding program
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Future challenges• Improved cost-efficiency
– Optimization, simplification of methods and future innovation
• Design of efficient and effective MAS strategies
• Greater integration between molecular genetics and plant breeding
• Data management
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Future of MAS in rice?
• Most important staple for many developing countries
• Model crop species– Enormous amount of research in molecular
genetics and genomics which has provided enormous potential for marker development and MAS
• Costs of MAS are prohibitive so available funding will largely determine the extent to which markers are used in breeding
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Food for thought• Do we need to use DNA markers
for plant breeding?
• Which traits are the highest priority for marker development?
• When does molecular breeding give an important advantage over conventional breeding, and how can we exploit this?
• How can we further minimize costs and increase efficiency?
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